Computo Journal Format

1 Introduction

This is a dummy example only for the purpose to use this repo as a template starter for creating new formats.

2 Structure of this repository

Everything for the extensions is in _extensions. See Quarto doc for details.

• In partials, you’ll find the .tex partials that can be used and should be removed or tweaked,s

• Your extension can make shortcodes and lua filters available. This document shows the effect of the one provided in the aft format.

• aft format sets some defaults which are different from pdf or html, link setting links to URL in read inside PDF output.

Source repository for this template format can found on Github

2.1 _extensions\aft

In this folder you’ll find everything that defines the extensions which could be installed using quarto install extension or be part of the template when using quarto use template

Format Metadata

This is in _extension.yml is where all the metadata about the format are defined so that Quarto knows what to use. Adapt this file for you own template.

Partials

In partials, there are the .tex files that will be used as Pandoc’s template. We provide here all the partials supported by Quarto and custom one for this format. Quarto allows to provide partials to ease the process of tweaking the default latex Pandoc’s template and keeping it up to date.
This template repo contains all the relevant partials that you can use with Quarto as example. We only tweaked title.tex to show the usage of a custom partials called _custom.tex.
Only keep the partials that you need to tweak for the format you are creating

If you need to completely change the default template (i.g customizing partials is not enough), then you need to provide your own template to Pandoc based on template.tex and also using partials or not. This can be provided using the template YAML key in _extension.yml for Quarto to use it.

This is considered advanced configuration as it will be harder to maintain than only using partials but could be required for some specific format. Be aware that this may lead to loose some Pandoc or Quarto features tied to default template.tex content if you remove some specific parts.

Lua Filters

Most of the time, custom formats will need Lua filters to provide specific features like cross format supports or provides custom shortcodes through the Quarto extension mechanism. Those filters will be available to the user and could be used in the custom formats (according to _extensions metadata). We have provided two examples:

• color-text.lua, a Lua filter used to add color to inline text for PDF and HTML outputs using the same Markdown syntax
• shorcodes.lua, a Lua filter which follow Quarto custom shortcodes guidelines to provide a {{< LaTeX >}} shortcode to nicely print LaTeX in PDF and HTML.

Remove or replace with your own Lua filters

Format resources

Resources required by the format needs to be available. We have provided two examples:

• te.bst is a biblio style file for demo. It has been downloaded from https://www.economics.utoronto.ca/osborne/latex/TEBST.HTM (http://econtheory.org/technical/te.bst) - Licence LPPL
• aft.cls is a dummy class file for this example format. It is a copy of official article.cls, the one provided in LaTeX installation (i.e at kpsewhich article.cls) and renamed as example (Licence LaTeX Project Public License)
• custom.scss is a style file to have a custom theme for our HTML format so that our Lua filter feature color-tex.lua works.

Those files are referenced within the _extension.yml to be used with our example format.

Remove and replace with your own resources

.quartoignore

Sometimes it is useful to have some files only needed for reference or for development. They should be available in the source repository but not downloaded to the user when quarto use template is used.

Use .quartoignore to register such file and folder (one file or folder per line)

style-guide folder

For quarto-journals format, use style-guide folder to include any documentation and resourced used for format creation, like a journal style guide or original .tex template. This folder is already added in .quartoignore in this example repo.

Remove, rename or add to this folder

template.qmd

This file is the template document that shows how to use the custom format. It will be downloaded with other resource by quarto use template, and even offered to be renamed if the name template.qmd is used.

This file will usually use the custom format (here aft-pdf and aft-html) and show how to use the template. When you’ll copy this template, you should be able to render this document to the demo format.

Adapt this file to provide a suitable template for your custom format

Other files

Other files are needed by the template and are usually user provided - they are not part of the custom format.

Here bibliography.bib is here to demo the usage of the bst file from the custom format.

Remove this file and provide a suitable one for your template

3 Checklist: Creating a custom format

Here is the checklist to help you know what to modify:

• Read the resources mentioned at the top,
• Use this template repo to create a new repository for your format (Click on “Use this template” to create new github repo)
• Once you are acquainted with the content, remove the resources that are there only as example (see above)
• Update README by replacing aft and Article Format Template mentions for your journal format
• Keep only the template partials that you need to tweak, and add custom ones if needed
• Add any Lua filters for shortcodes and other that would be useful to create the expected output format
• Add any external resource your format will need, and that should be part of the extension format that will be downloaded,
• Check _extension.yml is updated correctly
• Modify the skeleton template.qmd to your format and add any required resources to be downloaded to user.
• Check .quartoignore is updated which everything that should not be downloaded.
• Publish a demo of you format to github pages of the repo by using quarto publish command

4 Demo of some features found in this demo journal template

4.1 Shortcode demo

PDF are rendered using \LaTeX but it is best if one can use a Markdown syntax for cross format support.

\LaTeX used in source is a shortcode syntax where the shortcode is included in the extension folder _extensions

4.2 Code chunk

This format hide chunks by default as option has been set in _extension.yml file.

But you can set echo option to true locally in the chunk

Show the code

m_pois <- glm(Days ~ (Eth + Sex + Age + Lrn)^2, data = quine, family = poisson)
summary(m_pois)

Call:
glm(formula = Days ~ (Eth + Sex + Age + Lrn)^2, family = poisson, 
    data = quine)

Deviance Residuals: 
    Min       1Q   Median       3Q      Max  
-7.6533  -2.7796  -0.5301   1.5749   8.1955  

Coefficients: (1 not defined because of singularities)
            Estimate Std. Error z value Pr(>|z|)    
(Intercept)  2.93246    0.09826  29.843  < 2e-16 ***
EthN        -0.17399    0.12134  -1.434   0.1516    
SexM        -0.71452    0.12229  -5.843 5.14e-09 ***
AgeF1       -0.04270    0.12691  -0.336   0.7365    
AgeF2       -0.08632    0.16164  -0.534   0.5933    
AgeF3       -0.15290    0.11898  -1.285   0.1987    
LrnSL        0.21608    0.14558   1.484   0.1377    
EthN:SexM    0.43902    0.09208   4.768 1.86e-06 ***
EthN:AgeF1  -0.92889    0.14657  -6.337 2.34e-10 ***
EthN:AgeF2  -1.33398    0.13504  -9.879  < 2e-16 ***
EthN:AgeF3  -0.11242    0.13478  -0.834   0.4042    
EthN:LrnSL   0.26415    0.11378   2.322   0.0203 *  
SexM:AgeF1  -0.05565    0.16303  -0.341   0.7328    
SexM:AgeF2   1.09942    0.15281   7.195 6.26e-13 ***
SexM:AgeF3   1.15949    0.13859   8.366  < 2e-16 ***
SexM:LrnSL   0.04143    0.13718   0.302   0.7627    
AgeF1:LrnSL -0.13019    0.15688  -0.830   0.4066    
AgeF2:LrnSL  0.37340    0.14563   2.564   0.0103 *  
AgeF3:LrnSL       NA         NA      NA       NA    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for poisson family taken to be 1)

    Null deviance: 2073.5  on 145  degrees of freedom
Residual deviance: 1368.7  on 128  degrees of freedom
AIC: 1993.1

Number of Fisher Scoring iterations: 5

4.3 Text color

Our format makes applying color on inline text possible using the [content]{color=<name>} syntax. Let’s see an example.

Here we are using a special feature of our format which is the coloring because pink is a nice color.

This is possible thanks to the Lua Filter included in the custom extension format.

Using references

I did not read this book (CameronTrivedi2013?) but it must be interesting.

5 Introduction

5.1 About this document

This document provides a template based on the quarto system for contributions to Computo Computo Team (2021). We show how Python (Perez et al. 2011) or R (R Core Team 2020) code can be included.

5.2 Advice for writting your manuscript

First make sure that you are able to build your manuscript as a regular notebook on your system. Then you can start configure the binder environment.

6 Formatting

This section covers basic formatting guidelines. Quarto is a versatile formatting system for authoring HTML based on markdown, integrating \LaTeX and various code block interpreted either via Jupyter or Knitr (and thus deal with Python, R and many other langages). It relies on the Pandoc Markdown markup language.

To render/compile a document, run quarto render. A document will be generated that includes both content as well as the output of any embedded code chunks within the document:

quarto render content.qmd # will render to html

6.1 Basic markdown formatting

Bold text or italic

• This is a list
• With more elements
• It isn’t numbered.

But we can also do a numbered list

1. This is my first item
2. This is my second item
3. This is my third item

6.2 Mathematics

6.2.1 Mathematical formulae

LaTeX code is natively supported¹, which makes it possible to use mathematical formulae:

will render

f(x_1, \dots, x_n; \mu, \sigma^2) = \frac{1}{\sigma \sqrt{2\pi}} \exp{\left(- \frac{1}{2\sigma^2}\sum_{i=1}^n(x_i - \mu)^2\right)}

It is also posible to cross-reference an equation, see Equation 1:

\begin{aligned} D_{x_N} & = \frac12 \left[\begin{array}{cc} x_L^\top & x_N^\top \end{array}\right] \, \left[\begin{array}{cc} L_L & B \\ B^\top & L_N \end{array}\right] \, \left[\begin{array}{c} x_L \\ x_N \end{array}\right] \\ & = \frac12 (x_L^\top L_L x_L + 2 x_N^\top B^\top x_L + x_N^\top L_N x_N), \end{aligned} \tag{1}

6.2.2 Theorems and other amsthem-like environments

Quarto includes a nice support for theorems, with predefined prefix labels for theorems, lemmas, proposition, etc. see this page. Here is a simple example:

Theorem 1 (Strong law of large numbers) The sample average converges almost surely to the expected value:

\overline{X}_n\ \xrightarrow{\text{a.s.}}\ \mu \qquad\textrm{when}\ n \to \infty.

See Theorem 1.

6.3 Code

Quarto uses either Jupyter or knitr to render code chunks. This can be triggered in the yaml header, e.g., for Jupyter (should be installed on your computer) use

---
title: "My Document"
author "Jane Doe"
jupyter: python3
---

For knitr (R + knitr must be installed on your computer)

---
title: "My Document"
author "Jane Doe"
---

You can use Jupyter for Python code and more. And R + KnitR for if you want to mix R with Python (via the package reticulate Ushey et al. (2020)).

6.3.1 R

R code (R Core Team 2020) chunks may be embedded as follows:

Show the code

x <- rnorm(10)

6.3.2 Python

---
title: "My Document"
author "Jane Doe"
jupyter: python3
---

7 Figures

Plots can be generated as follows:

Interactive plots may also be produced in the HTML output of the document:

It is also possible to create figures from static images:

Figure 1: SFdS logo (c.a. 2021)

7.1 Tables

Tables (with label: @tbl-mylabel renders Table 1) can be generated with markdown as follows

Table 1: my table caption

Tables	Are	Cool
col 1 is	left-aligned	$1600
col 2 is	centered	$12
col 3 is	right-aligned	$1

Table can also be generated by some code, for instance with knitr here:

Table caption.

	speed	dist
	Min. : 4.0	Min. : 2.00
	1st Qu.:12.0	1st Qu.: 26.00
	Median :15.0	Median : 36.00
	Mean :15.4	Mean : 42.98
	3rd Qu.:19.0	3rd Qu.: 56.00
	Max. :25.0	Max. :120.00

7.2 Algorithms

A solution to typeset pseudocode just like you would do with \LaTeX, yet with HTML output is to rely on the JavaScript peudocode.js. Your pseudocode is written inside a <pre> tag. You need to modify the file includes/pseudocode-footer.html so that the Id of the rendered element match the one in <pre id ="">. The result is as follows:

\begin{algorithm}
\caption{A simple Algorithm}
\begin{algorithmic}
\STATE \textbf{Data}: $\mathcal{X} = \{x_1, \dots, x_n\}$
\STATE optimization parameters: number of iterations $T$, learning rate $\eta$
\STATE \textbf{Result}: output $\mathcal{Y} = \{y_1, \dots, y_n\}$
\PROCEDURE{myproc}{$T$, $\eta$}
    \FOR{$t = 0$ \TO $T$}
        \STATE do something (and fast please)
    \ENDFOR
\ENDPROCEDURE
\end{algorithmic}
\end{algorithm}

7.3 Handling references

7.3.1 Bibliographic references

References are displayed as footnotes using BibTeX, e.g. [@computo] will be displayed as (Computo Team 2021), where computo is the bibtex key for this specific entry. The bibliographic information is automatically retrieved from the .bib file specified in the header of this document (here:references.bib).

7.3.2 Other cross-references

As already (partially) seen, Quarto includes a mecanism similar to the bibliographic references for sections, equations, theorems, figures, lists, etc. Have a look at this page.

Bibliography

Computo Team (2021), “Computo: Reproducible computational/algorithmic contributions in statistics and machine learning,” computo.

Perez, F., Granger, B. E., and Hunter, J. D. (2011), “Python: An ecosystem for scientific computing,” Computing in Science
& Engineering, AIP Publishing, 13, 13–21.

R Core Team (2020), R: A language and environment for statistical computing, Vienna, Austria: R Foundation for Statistical Computing.

Ushey, K., Allaire, J., and Tang, Y. (2020), Reticulate: Interface to python.

Footnotes

1. We use katex for this purpose.

Reuse

https://creativecommons.org/licenses/by/4.0/